I don't use .bat files either. I just use a shortcut with specific parameters for each instance; and yes, they're conveniently placed on the desktop. In my case, I run the BE array first with its specific shortcut while the BFL device is turned off. When the BE array is running and has settled, I then turn on the BFL device and run its specific shortcut. Though the BFL device would run with the BE array in one instance using the BE-specific shortcut (-S all), BFGMiner would identify its chips as BE devices and would label it as such (ICA##).
Just an update on your method of managing BEs and BFL on the same machine. I found myself in exact situation after getting rid of one of my rigs. I created a script that allows me to disable the BFL, run BFGMiner for BEs only, then enable BFL and start the second instance with BFL only.
It's a simple script but with my GPUs, wait times for all com ports to register it's a good 5 minutes long startup procedure - still beats turning off BFL. If you're interested I can give you my script and some instructions to work on.